Processing and analysing omics datasets poses many challenges to life scientists, particularly when we need to share our methods with other researchers and scale up our research. Public and reproducible bioinformatics workflows, like those developed by nf-core, are invaluable resources for the life science community.

nf-core is a community-driven effort to provide high-quality bioinformatics workflows for common analyses including, RNAseq, mapping, variant calling, and single cell transcriptomics. A big advantage of using nf-core workflows is the ability to customise and optimise them for different computational environments, types and sizes of data and research goals.

This workshop will set you up with the foundational knowledge required to run and customise nf-core workflows in a reproducible manner. On day 1 you will learn about the nf-core tools utility, and step through the code structure of nf-core workflows. Then on day 2, using the nf-core/rnaseq workflow as an example, you will explore the various ways to adjust the workflow parameters, customise processes, and configure the workflow for your computational environment.

Lead Trainers

Dr Georgina Samaha, Senior Bioinformatician, Sydney Informatics Hub, University of Sydney

Dr Cali Willet, Senior Bioinformatician, Sydney Informatics Hub, University of Sydney

Dr Chris Hakkaart, Developer Advocate, Sequera Labs.

Date/Time

18 and 19 May 2023, 1-4pm AEST/12:30-3:30pm ACST/11am -2pm AWST

Format

This online workshop will take place over two sessions. You must attend both sessions to get the most out of the workshop. Expert trainers will introduce the topics and guide you through hands-on activities to help you put your new skills into action.

Learning outcomes

By the end of the workshop you should be able to:

• Recognise how Nextflow and nf-core enable reproducible and portable bioinformatics
• Write and run a basic nf-core run command
• Describe nf-core code/directory structure (config, modules, submodules, workflow, main.nf)
• Adjust the run command to customise the workflow
• Describe Nextflow configuration hierarchy
• Create and use a params file to customise workflow parameters
• Create and use a custom config file to adjust resource usage
  
• Apply external arguments not available as a workflow parameter to a process

Who the workshop is for

This workshop is for researchers and bioinformaticians who are already (or soon will) be using and customising nf-core workflows.

The workshop will be conducted in a Unix environment. Command line experience is required. Prior experience running Nextflow and nf-core workflows is recommended.

You must be associated with an Australian organisation for your application to be considered.

If you’re looking for an introduction to the fundamentals of Nextflow and nf-core you can watch our webinar Portable, reproducible and scalable bioinformatics workflows using Nextflow and Pawsey Nimbus Cloud or recordings of recent nf-core training.

How to apply

Apply here

This workshop is free but participation is subject to application with selection.

Applications close at 11:59pm AEST, Thursday 4 May 2023.

Applications will be reviewed by the organising committee and all applicants will be informed of the status of their application (successful, waiting list, unsuccessful). Successful applicants will be provided with a Zoom meeting link closer to the date. More information on the selection process is provided in our Advice on applying for Australian BioCommons workshops.

This workshop is presented by the Australian BioCommons, Sydney Informatics Hub and Sequera with the assistance of a network of facilitators from the national Bioinformatics Training Cooperative.

This event is part of a series of bioinformatics training events. If you'd like to hear when registrations open for other events, please subscribe to Australian BioCommons